Just wondering how to perform multiple sequence alignment for extremely long sequences, say several Mbs or even more than that. Any specific tool designed to do this? Thanks :)
Hello Yong Jia
Have you ever tried Clustalx? It contains matrices for the alignment of both protein and DNA sequences.
Clustal omega can do this. Jalview can also do this using clustalw. But for convenience I would suggest to analyse the gene assemblies first, for these long sequences, followed by alignment.
Thanks for these answers. I guess MAFFT may suit my purpose as it can handle
∼20 sequences × ∼1,000,000 bases (~15Mb);
I had a quick search for the seq size limit for the following tools:
clustal: up to 4000 sequences or a maximum file size of 4 MB
Kalign: up to 2000 sequences or a maximum file size of 2 MB
muscle: up to 500 sequences or a maximum file size of 1 MB
T-coffee: up to 500 sequences or a maximum file size of 1 MB
Other than that, LASTZ can align two sequences of chromosome scale but only for pair-wise alignment using one as a reference seq.
Hello Yong Jia
You can use Mauve, it is used to study of large-scale evolutionary events as invertions
http://darlinglab.org/mauve/mauve.html
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